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Spanish army Brig. Gen. D. Luis Martín-Rabadán, left, walks with Canadian Brig. Gen. Steve Whelan, centre, and Australian Brig. Gen. Rupert Hoskin during a battlefield circuit at the Besmaya Range Complex, Iraq, on Aug. 9, 2017.U.S. Army photo by Sgt. Tracy McKithern/AB Forces News Collection / Alamy Stock Photo

The Canadian Forces’ chief of military personnel is being investigated for sexual misconduct by military police and went on leave effective immediately on Friday – months after the probe was launched.

Lieutenant-General Steven Whelan was promoted to his current rank and placed in charge of military personnel and rooting out bad behaviour in the Forces in May. He replaced Vice-Admiral Haydn Edmundson, who went on leave in March while military police investigate a sexual-misconduct complaint against him.

A growing number of the Armed Forces’ most senior officers are facing sexual-misconduct complaints. While most of the individuals implicated in cases that are publicly known went on leave while the investigations are completed, Lt.-Gen. Whelan did not until The Globe and Mail asked about the investigation on Friday.

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“The Canadian Forces National Investigation Service received an allegation of sexual misconduct against Lieutenant-General Steven Whelan. The investigation is ongoing and no further information can be released,” the investigative body said in a statement.

The government and Canadian Forces confirmed Friday that Defence Minister Harjit Sajjan and acting chief of the defence staff General Wayne Eyre have known about the case since June 2.

Lt.-Gen. Whelan did not respond to a request for comment on Friday. The complaint against him was filed with military police in May, shortly after he was appointed to his new role, a source with direct knowledge of the matter told The Globe and Mail.

The complainant served under Lt.-Gen. Whelan’s command when the incidents allegedly occurred and was working under his command until he went on leave on Friday, the source said.

The Globe and Mail is not disclosing the source’s name because they were not cleared to speak publicly about the case.

“The minister requested that the complainant receive all necessary support. Decisions around investigations are determined by [the Canadian Forces National Investigation Service],” Mr. Sajjan’s spokesperson Daniel Minden said in a brief statement. He would not comment further because of the investigation.

The Military Personnel Command, which was led by Lt.-Gen. Whelan, is responsible for all matters pertaining to the management of military personnel. That includes recruitment, career management and eliminating “harmful and inappropriate behaviour” in the Canadian Forces, according to its website.

In a statement on Friday, the Canadian Armed Forces said the military police are investigating “historic allegations concerning Lt.-Gen. Whelan.”

Vice-chief of the defence staff Lieutenant-General Frances Allen has continually assessed Lt.-Gen. Whelan’s case “in regards to victim impact, his continuing employment, and impact on the workplace,” the statement said.

“Given recent developments, after discussing with the vice-chief of the defence staff, Lt.-Gen. Whelan agrees he must step aside as the Commander, Military Personnel, effective immediately,” the statement said.

Since February, the military has been gripped in a crisis over its inability to manage sexual-harassment cases within its ranks, as a growing number of senior officers have gone on leave while investigations against them are carried out.

On Wednesday, the military confirmed that Lieutenant-General Trevor Cadieu has been on leave since Sept. 5 while a sexual-misconduct complaint against him is investigated. In his case, Lt.-Gen. Cadieu went on leave the same day Gen. Eyre was notified of the investigation. Lt.-Gen. Cadieu was supposed to be appointed army commander on Sept. 7 but that was postponed indefinitely while the investigation plays out.

In a statement on Friday, the national investigation service said “Military Police do not, by practice, proactively disclose the existence of ongoing investigations” because “disclosing if someone is being investigated could jeopardize the integrity of the investigation.”

On Friday, The Globe reported on criticisms from military observers and opposition parties over the lack of transparency from the Armed Forces, in particular for cases involving senior officers, and the public’s lack of faith in the organization’s ability to manage the current crisis.

In the past nine months, former chief of the defence staff Jonathan Vance and his successor, Admiral Art McDonald, have been investigated. Both probes ended without charges related to the allegations. However, Mr. Vance was charged with obstruction of justice in connection to the misconduct investigation.

Adm. McDonald is on leave while the government conducts a separate probe. Major-General Dany Fortin is also on leave and faces one charge of sexual assault, which he denies.

News of the investigation into Lt.-Gen. Cadieu follows on the heels of the military reversing a decision to put Major-General Peter Dawe in charge of reviewing ways to eliminate sexual misconduct in the forces, after he had been on leave for writing a positive character reference for an officer convicted of sexual assault.

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